AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_bbur_reg_100.orf -o00230_bbur_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BB0416 24 pheromone shutdown protein (traB) BB0481 21 ribosomal protein L2 (rplB) Input sequences: #1 BB0196 300 peptide chain release factor 1 (prfA) #2 BB0239 300 deoxyguanosine/deoxyadenosine kinase(I) subunit 2 (dck) #3 BB0347 183 fibronectin/fibrinogen-binding protein, putative #4 BB0348 97 pyruvate kinase (pyk) #5 BB0389 82 DNA-directed RNA polymerase (rpoB) #6 BB0390 70 ribosomal protein L7/L12 (rplL) #7 BB0393 51 ribosomal protein L11 (rplK) #8 BB0394 23 transcription antitermination factor (nusG) #9 BB0395 108 preprotein translocase subunit (secE) #10 BB0414 248 chemotaxis protein methyltransferase (cheR-2) #11 BB0415 32 protein-glutamate methylesterase (cheB-1) #12 BB0417 36 adenylate kinase (adk) #13 BB0438 240 DNA polymerase III, subunit beta (dnaN) #14 BB0461 300 DNA polymerase III, subunits gamma and tau (dnaX) #15 BB0463 170 nucleoside-diphosphate kinase (ndk) #16 BB0476 300 translation elongation factor TU (tuf) #17 BB0477 50 ribosomal protein S10 (rpsJ) #18 BB0478 35 ribosomal protein L3 (rplC) #19 BB0488 21 ribosomal protein L14 (rplN) #20 BB0544 202 phosphoribosyl pyrophosphate synthetase (prs) #21 BB0551 220 chemotaxis response regulator (cheY-1) #22 BB0578 252 methyl-accepting chemotaxis protein (mcp-1) #23 BB0579 88 DNA polymerase III, subunit alpha (dnaE) #24 BB0776 178 B. burgdorferi predicted coding region BB0776 #25 BB0777 61 adenine phosphoribosyltransferase (apt) #26 BB0804 198 ribosomal protein S15 (rpsO) #27 BBK17 77 adenine deaminase (adeC) #28 BBB17 24 IMP dehydrogenase (guaB) #29 BBB18 184 GMP synthase (guaA) Motif number 1 ********** No masking Map Score: 7.77577e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 TTTTTTCATGTTTTTTTATATAATAAATGT 1 110 0 TTTTTTTATA 0.837925 -191 ATATAATTGATTTTTTTAATCACGCTTATT 1 139 1 TTTTTTTAAT 0.938283 -162 TAATTTTAGATTTTTTTGTTAGACTTTTTA 1 246 0 TTTTTTTGTT 0.830876 -55 AATTTTATTTTGTTTTTTGCAAGA 2 5 1 TTATTTTGTT 0.788483 -296 ATGGTTAGAATTTTTTTATTTTAGTCTCTT 2 34 1 TTTTTTTATT 0.886769 -267 AAAAATTAATTTTTTTTAATAAAAGAGACT 2 56 0 TTTTTTTAAT 0.938283 -245 ATATTAAATATAATTTTAATAAGGCTTTTA 2 90 0 TAATTTTAAT 0.913248 -211 TTTAATATCTTATTTTTAATTAAGATTAAT 2 112 1 TATTTTTAAT 0.932768 -189 TAAGAATTTTAATTTTTAAATTATGAATTT 2 152 1 AATTTTTAAA 0.851867 -149 TTGTTTAAGGATTTTTTGTTTTATATTAAA 2 194 1 ATTTTTTGTT 0.755183 -107 TCCAATGTAAAAATTTTAATATAAAACAAA 2 208 0 AAATTTTAAT 0.868591 -93 CTAAGCTTTAAATTTTTATTTTATGTATTA 3 137 0 AATTTTTATT 0.817761 -47 TTGAATAACAATATTTTGTAAAAAATTCAA 4 36 0 ATATTTTGTA 0.607095 -62 CCACTTTTATAAATTTTATGCTTTTTGTCA 4 66 0 AAATTTTATG 0.530781 -32 AACTTTGATATATTTTTAATTTT 5 4 0 TATTTTTAAT 0.932768 -79 TGTTAGTCTTAATTTTTGAGTGCATGCTAT 6 19 1 AATTTTTGAG 0.644826 -52 AGGTTTTTGTTTATTTTAATTTATTTGCAG 10 88 0 TTATTTTAAT 0.920228 -161 TTAATATAAGTAATTTTATTATAAGACATA 10 129 0 TAATTTTATT 0.844304 -120 GTAAGAATATTTTTTTTGAAAAAAAATTGT 10 163 0 TTTTTTTGAA 0.862939 -86 TAAATATTTGTTATTTTAAGGGT 12 4 0 TTATTTTAAG 0.793069 -33 GAATCAAAAATTATTTTAAACAATTGAACC 13 22 1 TTATTTTAAA 0.883928 -219 TTTTTTGTTGTATTTTTGATAAATTATTTG 13 51 0 TATTTTTGAT 0.896942 -190 TTGTAGGTTGTTTTTTTGTTGTATTTTTGA 13 62 0 TTTTTTTGTT 0.830876 -179 GTGGATTTTGTATTTTTATTTTTTATAGAT 13 175 0 TATTTTTATT 0.877251 -66 CGGTAAGCGATTTTTTTGATGAGTACGTAA 14 79 1 TTTTTTTGAT 0.905098 -222 GTCTTAGGTTTAATTTTGAACCCAAATGCA 14 109 1 TAATTTTGAA 0.813417 -192 ATTTTATTATATTTTTTATGTTTCATAAAA 14 187 1 ATTTTTTATG 0.6203 -114 TTTTTAATTTTGTAAAAGTTATAT 15 5 1 TAATTTTGTA 0.691901 -166 TGTAAAAGTTATATTTTGATTTTTCAATAC 15 21 1 ATATTTTGAT 0.819616 -150 AATCAGATATAATTTTTGTATTGAATAAGT 15 97 1 AATTTTTGTA 0.650143 -74 ATTGAATAAGTATTTTTATTTATTTAATTA 15 116 1 TATTTTTATT 0.877251 -55 TTTATTTAATTATTTTTAAATATATATCCT 15 134 1 TATTTTTAAA 0.901563 -37 AGCTTTATTTTTTAATATTTTGTGCT 16 7 1 ATTTTTTAAT 0.905175 -294 AGTTTATATTAATTTTTAATGCTATTATAT 16 55 1 AATTTTTAAT 0.897025 -246 CGTATTGACTATATTTTGTAAAATGTGTAG 16 114 1 ATATTTTGTA 0.607095 -187 TTTTTCTAAAAAATTTTAATAGCTTTAAAA 16 146 0 AAATTTTAAT 0.868591 -155 GATTTTTTTATTTTTTTGATTATTTGTAGC 16 206 1 TTTTTTTGAT 0.905098 -95 AGCTATTTTCTTATTTTAATAAGAATAAAT 16 233 1 TTATTTTAAT 0.920228 -68 TTTGTTAAAAATTTTTTAAAGAGATTAAAT 16 262 1 ATTTTTTAAA 0.863045 -39 ATGATATTTTAAGTATATGAATT 18 4 1 ATATTTTAAG 0.706434 -32 TTTATTTAATTTTATTTTTAGGATTA 20 7 1 TAATTTTATT 0.844304 -196 TTTAGATTTTTATTTTTATTATTAAAGCTA 20 71 1 TATTTTTATT 0.877251 -132 TAAAGCTAAAATATTTTAATGACCTTGCTT 20 93 1 ATATTTTAAT 0.878687 -110 TATGACTAAAATTTTTTAAAGCAAGGTCAT 20 111 0 ATTTTTTAAA 0.863045 -92 TCTTTAAAGATTATTTTAATTTGAACATAA 21 121 0 TTATTTTAAT 0.920228 -100 AATGTGAATTATATTTTAATTGTCGTTAAA 21 182 1 ATATTTTAAT 0.878687 -39 GTCGTTAAAGATATTTTAATATGCTAGA 21 203 1 ATATTTTAAT 0.878687 -18 AATTTAAAACTAATTTTAAATTAAAT 22 7 0 TAATTTTAAA 0.874206 -246 ATGTAAAAATATTTTTTGTTTATTGATGTA 22 144 1 ATTTTTTGTT 0.755183 -109 CATAAAAACTTTTTTTTGAATAGGGTCACC 22 220 0 TTTTTTTGAA 0.862939 -33 TTATTTTGATAAGATTTGTT 23 1 1 TTATTTTGAT 0.878591 -88 AAGTCATAATAATTTTTAAATCTCTAATTT 23 41 0 AATTTTTAAA 0.851867 -48 TGACTTTTTTAATTTTTATTTATTTGATTA 23 65 1 AATTTTTATT 0.817761 -24 TGTTTTTGCTTAATTTTATATTTTTTTGTC 24 33 1 TAATTTTATA 0.781652 -146 ACTTATTTTATAATTTTAATTATTAAGATA 24 71 0 TAATTTTAAT 0.913248 -108 GTTTGTGGCTAATTTTTAAATTAGCTGCCT 24 112 1 AATTTTTAAA 0.851867 -67 ATTATAGCTCTTTTTTTAAATTACTCATGT 24 143 0 TTTTTTTAAA 0.90939 -36 TATGACATTTTAATTTTATATTTGTTTTTT 26 23 1 TAATTTTATA 0.781652 -176 TTTATATTTGTTTTTTTAAACAATTTAATA 26 37 1 TTTTTTTAAA 0.90939 -162 CTTTTCGGGTTATTTTTAATAATAAATTAT 26 64 0 TATTTTTAAT 0.932768 -135 TTGCTTTTGTTATTTTTAAGAAAAAATATT 26 100 1 TATTTTTAAG 0.821724 -99 ATCGTAGTAGTTATTTTAAATTATGGCAAG 26 137 1 TTATTTTAAA 0.883928 -62 TTTTCTAAAAAATTTTTAAATCTTTCTACT 27 19 0 AATTTTTAAA 0.851867 -59 AATTTGGTTCTTTTTTTAAGAGATTTTTAA 29 77 1 TTTTTTTAAG 0.834736 -108 AAGAGATTTTTAATTTTAAATTTCTTGTTT 29 94 1 TAATTTTAAA 0.874206 -91 ********** Masking position 5 Map Score: 88.5138 Number of sites scoring better than the average of aligned sites = 3353 Number in coding regions = 2150 Number in noncoding regions = 1203 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 AAAACCTAATTTAACTTTAATATCCAACTTA 1 76 1 TTACTTTAAT 0.668698 -225 TCCAACTTAATAACATTTATTATATAAAAAA 1 98 1 TAAATTTATT 0.882479 -203 AAAAAATCAATTATATTTTTTCATGTTTTTT 1 124 0 TTAATTTTTT 0.905021 -177 TATATTAATTTTAGATTTTTTTGTTAGACTT 1 250 0 TTAATTTTTT 0.905021 -51 TAGTAATAGTTTATATTAATTTTAGATTTTT 1 261 0 TTAATTAATT 0.869516 -40 GCAAGATGGTTAGAATTTTTTTATTTTAGTC 2 29 1 TAGATTTTTT 0.615918 -272 CTTATTAAAATTATATTTAATATCTTATTTT 2 97 1 TTAATTTAAT 0.893803 -204 TTATTGACATTAATCTTAATTAAAAATAAGA 2 119 0 TAACTTAATT 0.409991 -182 ATTTCTTTTCTAAAATTTGTTTAAGGATTTT 2 178 1 TAAATTTGTT 0.740269 -123 AATTTTTACATTGGATTTTTTCATTAATGAA 2 223 1 TTGATTTTTT 0.786686 -78 GTTCTTTTTTTTAGCTTATATTTGAATTTAT 2 270 1 TTACTTATAT 0.300575 -31 TAGCTTATATTTGAATTTATTTAAGTTATT 2 281 1 TTGATTTATT 0.869856 -20 TTATTGTCAATAAACTTTATTTCCATAATAC 3 66 1 TAACTTTATT 0.642961 -118 AAGTAAAGTTTTGAATTTTTTACAAAATATT 4 26 1 TTGATTTTTT 0.786686 -72 AAGCTCCCATTAGTATTAAATT 7 2 0 TAGATTAAAT 0.353407 -50 TTTTGTTTATTTTAATTTATTTGCAGCAATA 10 83 0 TTTATTTATT 0.653485 -166 ATAAAATTACTTATATTAATTTTACAATTTT 10 140 1 TTAATTAATT 0.869516 -109 GATTGTTTAATTGTATTTAATACTATATGAT 13 113 0 TTGATTTAAT 0.765118 -128 ATATATTCTATTACATTTTATCTTAATAAGA 13 209 0 TTAATTTTAT 0.822819 -32 TTCAATTTTATTATATTTTTTATGTTTCATA 14 183 1 TTAATTTTTT 0.905021 -118 GAATAAGTATTTTTATTTATTTAATTATTTT 15 119 1 TTTATTTATT 0.653485 -52 AATATAAACTTTACATTAATTAAAGAAAAGC 16 34 0 TTAATTAATT 0.869516 -267 AATGTAAAGTTTATATTAATTTTTAATGCTA 16 48 1 TTAATTAATT 0.869516 -253 TTAAAGCTATTAAAATTTTTTAGAAAAACAC 16 148 1 TAAATTTTTT 0.805572 -153 AAATAGCTACTTACATTTAATCTCTTTAAAA 16 275 0 TTAATTTAAT 0.893803 -26 ATCCTAAAAATAAAATTAAATAAA 20 4 0 TAAATTAAAT 0.585439 -199 GATTATGTTATAGTATTTGTTTTTGCTATTA 20 32 1 TAGATTTGTT 0.524513 -171 TTAAAATATTTTAGCTTTAATAATAAAAATA 20 81 0 TTACTTTAAT 0.668698 -122 CAAATATGACTAAAATTTTTTAAAGCAAGGT 20 114 0 TAAATTTTTT 0.805572 -89 AAAACTAATTTTAAATTAAAT 22 1 0 TTAATTAAAT 0.764578 -252 AAAATTAGTTTTAAATTAAATTAAATTAAAT 22 20 1 TTAATTAAAT 0.764578 -233 TTAAATTAAATTAAATTAAATGAGGAGAATG 22 35 1 TTAATTAAAT 0.764578 -218 AGATGAAAGCTTAAATTTATTTCAAAGTAAT 22 96 1 TTAATTTATT 0.945263 -157 TTATTTTGATAAGATTTGTTGCAATAATTT 23 10 1 TAAATTTGTT 0.740269 -79 CTTTTTTAATTTTTATTTATTTGATTAAGGT 23 68 1 TTTATTTATT 0.653485 -21 TTGCTTAATTTTATATTTTTTTGTCTAGGTT 24 38 1 TTAATTTTTT 0.905021 -141 CATTTTAATTTTATATTTGTTTTTTTAAACA 26 28 1 TTAATTTGTT 0.867631 -171 CGATAGATTATAATATTTTTTCTTAAAAATA 26 110 0 TAAATTTTTT 0.805573 -89 GAGTGATGAATTAAATTTGATTATTGATAAT 29 49 1 TTAATTTGAT 0.761593 -136 ATTTTTAATTTTAAATTTCTTGTTTTAATGA 29 99 1 TTAATTTCTT 0.600462 -86 *** ******* Masking position 6 Map Score: 42.063 Number of sites scoring better than the average of aligned sites = 1562 Number in coding regions = 949 Number in noncoding regions = 613 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 TAAATTAGGTTTTGTTGTATTTATATATAAATTGAG 1 53 0 TTTGTTTTTT 0.876793 -248 GATGGTTAGAATTTTTTTATTTTAGTCTCTTTTATT 2 33 1 ATTTTTTTAT 0.820392 -268 TAATTTAAGAATTTTAATTTTTAAATTATGAATTTC 2 147 1 ATTTATTTAT 0.720846 -154 TTGTTTAAGGATTTTTTGTTTTATATTAAAATTTTT 2 194 1 ATTTTTTTTT 0.913982 -107 AAATTTTTACATTGGATTTTTTCATTAATGAAGTTT 2 222 1 ATTGATTTAT 0.68777 -79 ACAAAACTACATTTAAACTATTTATTGTCAATAAAC 3 45 1 ATTTAATTAT 0.657849 -139 ACTTTTATAAATTTTATGCTTTTTGTCATTGAATAA 4 58 0 ATTTATTTTT 0.867076 -40 TAAATCGACATTTGAAAACATTTTTTCCAACACTCA 10 33 1 TTTGAATTTT 0.749876 -216 TAAAAAGGTTTTTGTTTATTTTAATTTATTTGCAGC 10 87 0 TTTGTTTTAT 0.753644 -162 ACTTATATTAATTTTACAATTTTTTTTCAAAAAAAA 10 148 1 ATTTATTTTT 0.867076 -101 CGTTACTTTTTTCCCATTTTATTCTTGTTAAA 11 11 0 TTTTTATTTT 0.861393 -22 TGATAAATTATTTGGTTCAATTGTTTAAAATAATTT 13 29 0 TTTGTATTTT 0.830035 -212 ATTTTGTGGATTTTGTATTTTTATTTTTTATAGATA 13 174 0 TTTTTTTTTT 0.900558 -67 TAACTTTCAATTTTATTATATTTTTTATGTTTCATA 14 178 1 TTTTTATTTT 0.861393 -123 AAGTATTTTTATTTATTTAATTATTTTTAAATATAT 15 123 1 ATTTTATTTT 0.879397 -48 TTTTTTAATATTTTGTGCTTTTCTTTAATTAATGTA 16 18 1 TTTTTTTTTT 0.900558 -283 TTTCTAAAAAATTGATTTTTTTATTTTTTTGATTAT 16 193 1 ATTGTTTTTT 0.893045 -108 TTTTTGATTATTTGTAGCTATTTTCTTATTTTAATA 16 218 1 TTTGAATTTT 0.749876 -83 TTTAAAAAATTTTTAACAAATTTATTCTTATTAAAA 16 246 0 TTTTAATTAT 0.621219 -55 ATTTAATTTTATTTTTAGGATTATGTTATAGTATTT 20 14 1 ATTTTATTTT 0.879398 -189 TATTAATAGAATTTTTAGATTTTTATTTTTATTATT 20 58 1 ATTTTTTTTT 0.913983 -145 GTAAATTAAGATTGTTAAGATTTTCTAAAAAAGAAC 20 167 1 ATTGTATTTT 0.85141 -36 AGGGTAAAATTTAACATATTCTTTATTATTTTAT 21 9 1 ATTTAATTTT 0.817396 -212 TTTTGGTGGTATTTTACAGTTTGTATAGTAAAGTCG 21 69 0 ATTTATTTTT 0.867076 -152 TGTCTTTTTGATTGATATTTTTCTTTAAAGATTATT 21 136 0 ATTGTTTTTT 0.893044 -85 TAATTCACATTTTTATAATATTGTCTTTTTGATTGA 21 157 0 TTTTTATTTT 0.861393 -64 AACAAAAAATATTTTTACATTTAAATGGTAAAAATT 22 128 0 ATTTTTTTAT 0.820234 -125 TTTTTTGTTTATTGATGTATTTGATTTGATATTAAA 22 155 1 ATTGTTTTAT 0.782104 -98 CCAGTACTTAATTTGACACATTATTTCAACTTTTAA 22 186 0 ATTTAATTTT 0.817398 -67 TATTATGACTTTTTTAATTTTTATTTATTTGATTAA 23 60 1 TTTTATTTTT 0.847551 -29 TTTTGCTTAATTTTATATTTTTTTGTCTAGGTTTTT 24 36 1 TTTTTTTTTT 0.900558 -143 ATACAACTTATTTTATAATTTTAATTATTAAGATAA 24 70 0 TTTTTTTTAT 0.795625 -109 ATATTTGTTTTTTTAAACAATTTAATAATTTATTAT 26 40 1 TTTTAATTAT 0.621042 -159 ACCTCTCCATTTTTTTCTTATTTTCTAAAAAATTTT 27 33 0 TTTTTATTTT 0.861393 -45 GCATATCTATTGGACTATTTTTTT 28 1 0 ATTGATTTTT 0.836759 -24 CCCAAAAGATTTGTTATTTTTTTGTCAAATTTTTA 29 10 1 TTTGTTTTTT 0.876793 -175 TTTTTAAGAGATTTTTAATTTTAAATTTCTTGTTTT 29 89 1 ATTTTTTTAT 0.820234 -96 **** * *** * * Masking position 11 Map Score: 57.4144 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 1389 Number in noncoding regions = 742 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 TTTTCATGTTTTTTTATATAATAAATGTTA 1 108 0 TTTTTATATA 0.5364 -193 TTTAAAACTGCTTTTATTAAATAAATAGAA 1 167 0 CTTTTATTAA 0.774381 -134 TTTTAACATTCTTTTTTAAAACTGCTTTTA 1 181 0 CTTTTTTAAA 0.482364 -120 TTTGTTAGACTTTTTAATAAGTTTTGTGTA 1 232 0 TTTTTAATAA 0.259066 -69 ATAGTAATAGTTTATATTAATTTTAGATTT 1 263 0 TTTATATTAA 0.386329 -38 ATTTTAGTCTCTTTTATTAAAAAAAATTAA 2 51 1 CTTTTATTAA 0.774381 -250 AATAAGGCTTTTATTAGAAAAATTAATTTT 2 73 0 TTATTAGAAA 0.519903 -228 AATATCTTATTTTTAATTAAGATTAATGTC 2 115 1 TTTTAATTAA 0.24866 -186 TTATGAATTTCTTTTCTAAAATTTGTTTAA 2 172 1 CTTTTCTAAA 0.43459 -129 GATTTTTTGTTTTATATTAAAATTTTTACA 2 203 1 TTTATATTAA 0.386329 -98 ACATTGGATTTTTTCATTAATGAAGTTTTG 2 230 1 TTTTCATTAA 0.329786 -71 CTATGAACTCTTATTATTAAGCTTAAGCTA 3 12 1 TTATTATTAA 0.708589 -172 TGGAAATAAACTATTATTAATAGTACTAGT 3 106 1 CTATTATTAA 0.476776 -78 AGTTTTGAATTTTTTACAAAATATTGTTAT 4 32 1 TTTTTACAAA 0.58981 -66 TCTTCCTCCACTTTTATAAATTTTATGCTT 4 73 0 CTTTTATAAA 0.821883 -25 AACAAAAACCTTTTTATAAACCTATGTCTT 10 107 1 TTTTTATAAA 0.887287 -142 TAAGAATATTTTTTTTGAAAAAAAATTGTA 10 162 0 TTTTTTGAAA 0.452853 -87 CCTAAGAGATTTATTATAAATAGGCAATAC 10 192 1 TTATTATAAA 0.746627 -57 AGGCAATACTTATTTATAAAGAGAAGAATT 10 213 1 TATTTATAAA 0.296694 -36 GAATCAAAAATTATTTTAAACAATTGAACC 13 22 1 TTATTTTAAA 0.404692 -219 TTTGTTGTATTTTTGATAAATTATTTGGTT 13 48 0 TTTTGATAAA 0.395536 -193 GTATTTTTATTTTTTATAGATATATAGTAG 13 166 0 TTTTTATAGA 0.404963 -75 CAAAATATAACTTTTACAAAATTAAAAA 15 9 0 CTTTTACAAA 0.345408 -162 TGAATAAGTATTTTTATTTATTTAATTATT 15 118 1 TTTTTATTTA 0.462787 -53 TAATGTAAAGTTTATATTAATTTTTAATGC 16 47 1 TTTATATTAA 0.386329 -254 CTATTAAAATTTTTTAGAAAAACACGTAGT 16 154 1 TTTTTAGAAA 0.800703 -147 AAAAATCAATTTTTTAGAAATTGACCCGCA 16 183 0 TTTTTAGAAA 0.800703 -118 AACAAATTTATTCTTATTAAAATAAGAAAA 16 238 0 TTCTTATTAA 0.369606 -63 TTTTGATTTTTCTAAAGGAGG 19 7 1 TTTTTCTAAA 0.677523 -15 ATTTTTATTTTTATTATTAAAGCTAAAATA 20 76 1 TTATTATTAA 0.708589 -127 GTGTGTATAAGTTTTATTAATTAGTAAATT 20 144 1 GTTTTATTAA 0.362337 -59 TCCTCGTTCTTTTTTAGAAAATCTTAACAA 20 178 0 TTTTTAGAAA 0.800703 -25 ATAATTCACATTTTTATAATATTGTCTTTT 21 164 0 TTTTTATAAT 0.297819 -57 ACTTTTTTAATTTTTATTTATTTGATTAAG 23 67 1 TTTTTATTTA 0.462787 -22 ATTATAGCTCTTTTTTTAAATTACTCATGT 24 143 0 TTTTTTTAAA 0.718433 -36 TTTATATTTGTTTTTTTAAACAATTTAATA 26 37 1 TTTTTTTAAA 0.718433 -162 ATTTAATAATTTATTATTAAAAATAACCCG 26 59 1 TTATTATTAA 0.708589 -140 ATTATAATATTTTTTCTTAAAAATAACAAA 26 105 0 TTTTTCTTAA 0.610817 -94 ATCGTAGTAGTTATTTTAAATTATGGCAAG 26 137 1 TTATTTTAAA 0.404692 -62 ATTTAAAAATTTTTTAGAAAATAAGAAAAA 27 28 1 TTTTTAGAAA 0.800703 -50 ********** Masking position 2 Map Score: 21.1995 Number of sites scoring better than the average of aligned sites = 2617 Number in coding regions = 1574 Number in noncoding regions = 1043 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 ATATTAAAGTTAAATTAGGTTTTGTTGTATTT 1 67 0 TAAATAGTTT 0.505567 -234 AATATCCAACTTAATAACATTTATTATATAAA 1 94 1 TTAATACTTT 0.926182 -207 ATTGATTTTTTTAATCACGCTTATTCTATTTA 1 144 1 TTAATACCTT 0.883503 -157 GTTAGACTTTTTAATAAGTTTTGTGTAGATTC 1 227 0 TTAATAGTTT 0.934606 -74 AAATATAATTTTAATAAGGCTTTTATTAGAAA 2 83 0 TTAATAGCTT 0.896252 -218 GATTTTTTCATTAATGAAGTTTTGTTCGTTAG 2 236 1 TTAATAATTT 0.711868 -65 ACTAGTACTATTAATAATAGTTTATTTCCATG 3 104 0 TTAATATGTT 0.598937 -80 AATGAGGAATTTAATGAGTGTTGGAAAAAATG 10 51 0 TTAATAGGTT 0.896252 -198 ACATTTTATCTTAATAAGATTTTGTGGATTTT 13 196 0 TTAATAGTTT 0.934606 -45 TTATATCTGATTAATTACATTTATATGGAATA 15 77 0 TTAATACTTT 0.926182 -94 TTTTATTTATTTAATTATTTTTAAATATATAT 15 129 1 TTAATATTTT 0.711868 -42 CTAAAATATTTTAATGACCTTGCTTTAAAAAA 20 98 1 TTAATACTTG 0.800154 -105 AATTTACTAATTAATAAAACTTATACACACAA 20 142 0 TTAATAACTT 0.598937 -61 ATGGTAAAAATTAATTACTTTGAAATAAATTT 22 108 0 TTAATACTTG 0.800154 -145 TTATTTTGATAAGATTTGTTGCAATAA 23 6 1 TTGATAGTTT 0.644439 -83 TCAAATTTAATTCATCACTCTTGTAAAAATTT 29 37 0 TTCATACCTT 0.72053 -148 ATTTCTTGTTTTAATGAGATTGGGTCAGTTAT 29 113 1 TTAATAGTTG 0.820167 -72 CCCCAGTGATTTCATTAGTGTTAATAACGGTA 29 153 1 TTCATAGGTT 0.745985 -32 ATTGTTTCATTACCGTTATTAACACTA 29 168 0 TTCATACGTT 0.72053 -17 ***** ** *** Masking position 5 Map Score: 16.1688 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 74 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AATCAATTATATTTTTTCATGTTTTTTTAT 1 121 0 ATTTTTTCAT 0.803759 -180 TTTATGTTTTATTTTAACATTCTTTTTTAA 1 192 0 ATTTTAACAT 0.857756 -109 AAATAAAAAAATTCTAACCATCTTGCAAAA 2 25 0 ATTCTAACCA 0.74208 -276 TTATATTAAAATTTTTACATTGGATTTTTT 2 214 1 ATTTTTACAT 0.858491 -87 TTTACATTGGATTTTTTCATTAATGAAGTT 2 227 1 ATTTTTTCAT 0.803759 -74 ATCCTAATTCTTTCAAGGTGTTTATA 3 168 0 ATTCTTTCAA 0.778351 -16 CCTCACTTTAATTCTAACAACAGGTCAGGA 9 82 0 ATTCTAACAA 0.83876 -27 ATTTGAAAACATTTTTTCCAACACTCATTA 10 42 1 ATTTTTTCCA 0.733476 -207 TACTTATATTAATTTTACAATTTTTTTTCA 10 147 1 AATTTTACAA 0.718815 -102 CAAAAAAAATATTCTTACCTAAGAGATTTA 10 175 1 ATTCTTACCT 0.703122 -74 TGAACCAAATAATTTATCAAAAATACAACA 13 46 1 AATTTATCAA 0.633124 -195 AACAACCTACAATTTAACAAGATATTTACT 13 80 1 AATTTAACAA 0.718815 -161 AGGGTAAAATTTAACATATTCTTTATT 21 8 1 AATTTAACAT 0.677857 -213 ATTCTTTATTATTTTATCAAACAATTCTAA 21 28 1 ATTTTATCAA 0.832654 -193 TTATCAAACAATTCTAACAAGCAAAAACCG 21 41 1 ATTCTAACAA 0.83876 -180 AAAGTAATTAATTTTTACCATTTAAATGTA 22 119 1 ATTTTTACCA 0.803021 -134 AACAAAAAATATTTTTACATTTAAATGGTA 22 134 0 ATTTTTACAT 0.858491 -119 AAAGGGATTCTATCATAAAAACTTTT 22 237 0 ATTCTATCAT 0.742973 -16 TAACAAAAGCAATTTATCCTTTTCGGGTTA 26 82 0 AATTTATCCT 0.439995 -117 TTTTTGTCAAATTTTTACAAGAGTGATGAA 29 29 1 ATTTTTACAA 0.880535 -156 ********** Masking position 5 Map Score: 17.9586 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 403 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 TATATAAAAAAACATGAAAAAATATAATTGAT 1 118 1 ACATGAAAAA 0.637464 -183 CTAACCATCTTGCAAAAAACAAAATAAAATT 2 10 0 TCAAAAACAA 0.568826 -291 TTAAGCTATTAACAAAACTACATTTAAACTAT 3 34 1 ACAAAACACA 0.856472 -150 CAAGCCGCACATCATAACGACATGCGGAATAA 5 35 0 ACATAACACA 0.688888 -48 TTTAACAAGAATAAAATGGGAAAAA 11 4 1 ACAAGAAAAA 0.825741 -29 CAAATAATTTATCAAAAATACAACAAAAAAAC 13 51 1 ACAAAAAACA 0.949238 -190 TCCATATCTTAACATAAAGCAAAACATTGCAT 14 134 0 ACATAAACAA 0.78579 -167 AATTGAAAGTTACAAAAAGACAAATCCATATC 14 158 0 TCAAAAAACA 0.713913 -143 GCTACAAATAATCAAAAAAATAAAAAAATCAA 16 204 0 ACAAAAAATA 0.647043 -97 TTCTATTAATAGCAAAAACAAATACTATAACA 20 37 0 ACAAAAAAAA 0.928716 -166 AATTCTAACAAGCAAAAACCGACTTTACTATA 21 50 1 ACAAAAACGA 0.67338 -171 GTAAAATACCACCAAAAATACATGCTATTTTA 21 88 1 ACAAAAAACA 0.949238 -133 TTTTAATTTGAACATAAATAAAATAGCATGTA 21 106 0 ACATAAAAAA 0.828604 -115 AAAAATATCAATCAAAAAGACAATATTATAAA 21 150 1 ACAAAAAACA 0.949238 -71 TTCATCTTAAACCATAAAACCATCTAAAGATA 22 71 0 ACATAAACCA 0.840386 -182 AATCAAATACATCAATAAACAAAAAATATTTT 22 149 0 ACAATAACAA 0.614765 -104 TATAAAATTAAGCAAAAACACAACAGGCCAAT 24 21 0 ACAAAAAACA 0.949238 -158 TTTTTCAAATATCAAGACCAAAAGCCAAAT 25 9 0 ACAAGACAAA 0.601934 -53 GAACCAAATTATCAATAATCAAATTTAATTCA 29 55 0 ACAATAACAA 0.614765 -130 * ****** *** Masking position 7 Map Score: 15.7487 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 272 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 TTAAAAATTAAAATTCTTAAATTATTGACA 2 141 0 AAATTCTTAA 0.81401 -160 TTTAGAAAAGAAATTCATAATTTAAAAATT 2 162 0 AAATTCATAA 0.728159 -139 ATAAAACAAAAAATCCTTAAACAAATTTTA 2 188 0 AAATCCTTAA 0.803653 -113 AAAAAGCATAAAATTTATAAAAGTGGAGGA 4 70 1 AAATTTATAA 0.781547 -28 CAACTTTGATATATTTTTAATTTT 5 5 0 ATATTTTTAA 0.821103 -78 TGTGAAATGAAAATATATAAGGAGTTAAT 6 52 1 AAATATATAA 0.722121 -19 TTAAAATAACAAATATTTAAACAGGAGTAT 12 15 1 AAATATTTAA 0.809387 -22 TTACTACTATATATCTATAAAAAATAAAAA 13 163 1 ATATCTATAA 0.72428 -78 AATTTAGGATATATATTTAAAAATAATTAA 15 139 0 ATATATTTAA 0.769258 -32 TCTCTTTAAAAAATTTTTAACAAATTTATT 16 256 0 AAATTTTTAA 0.85392 -45 GAGTATTAATATATCCTTAAAGTCTTAAC 17 10 0 ATATCCTTAA 0.762682 -41 CCTCAAATTCATATACTTAAAATATCAT 18 9 0 ATATACTTAA 0.713978 -27 GCATATTAAAATATCTTTAACGACAATTAA 21 197 0 ATATCTTTAA 0.81105 -24 GATATTTGAAAAATATATAAACATATAGAT 25 28 1 AAATATATAA 0.722121 -34 ATGTCATAATATATTTATAA 26 1 0 ATATTTATAA 0.737456 -198 ATTTTCTAAAAAATTTTTAAATCTTTCTAC 27 20 0 AAATTTTTAA 0.85392 -58 ********** Masking position 4 Map Score: 13.882 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 588 Number in noncoding regions = 317 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 AAATTTAAAGCTTAGATATAAACACCTTGA 3 152 1 CTTAGATATA 0.814821 -32 CAAAACTTTACTTTGCTATAAGCAGTGT 4 9 0 CTTTGCTATA 0.965566 -89 GGAATAACAACTTTGATATATTTTTAATTT 5 12 0 CTTTGATATA 0.94691 -71 CAAAAACCGACTTTACTATACAAACTGTAA 21 62 1 CTTTACTATA 0.812689 -159 AAATTAATTACTTTGAAATAAATTTAAGCT 22 103 0 CTTTGAAATA 0.814821 -150 TTTGTTAGAGCTTTGCTATAATGGTATAGG 26 170 1 CTTTGCTATA 0.965566 -29 ********** Masking position 3 Map Score: 2.26858 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 9 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 GCTTTTATTAAATAAATAGAATAAGCGTGATTA 1 155 0 AATATGAATA 0.638656 -146 GTCTAACAAAAAAATCTAAAATTAATATAAACT 1 252 1 AAAATAAATT 0.798288 -49 GAAAGATAGTAATAGTTTATATTAATTTTAGAT 1 265 0 AATATATATT 0.696547 -36 AATTAAAAATAAGATATTAAATATAATTTTAAT 2 100 0 AAGATAAATA 0.397399 -201 TTCATAATTTAAAAATTAAAATTCTTAAATTAT 2 146 0 AAAATAAATT 0.79836 -155 AATAACTTAAATAAATTCAAATA 2 288 0 AATATAAATA 0.883416 -13 ATTGACAATAAATAGTTTAAATGTAGTTTTGTT 3 44 0 AATATAAATG 0.490056 -140 GTACTAGTTTAATACATAAAATAAAAATTTAAA 3 128 1 AATATAAATA 0.883338 -56 AAAATTAAAAATATATCAAAGTT 5 1 1 AAAAAAAATA 0.607667 -82 TATTGCTGCAAATAAATTAAAATAAACAAAAAC 10 83 1 AATATAAAAT 0.483373 -166 ACCCTTAAAATAACAAATATTTAAACAGGAG 12 9 1 AATAAATATT 0.500859 -28 TATATCTATAAAAAATAAAAATACAAAATCCAC 13 172 1 AAAAAAAATA 0.607672 -69 GATAAAATGTAATAGAATATATAAGGAGGCATC 13 218 1 AATAAATATA 0.481705 -23 CTGAGATATAAATATGTTGTATAGTATATATTT 14 236 1 AATATGTATA 0.31735 -65 CCTATGCTTTAATAAGTAAAATATTAGTAAATA 14 264 0 AATATAAATA 0.883416 -37 ATTTATATGGAATAATACAAATTATAAAGCACT 15 58 0 AATAAAAATT 0.791025 -113 AAAATAATTAAATAAATAAAAATACTTATTCAA 15 117 0 AATATAAAAT 0.483373 -54 TAATAGCATTAAAAATTAATATAAACTTTACAT 16 49 0 AAAATATATA 0.493148 -252 CTCAAATTCATATACTTAAAATATCAT 18 5 0 TATATAAATA 0.235011 -31 TAAAATACCTCAAATTCATATACTTA 18 20 0 AATATAAATT 0.893445 -16 TTTTAGCTTTAATAATAAAAATAAAAATCTAAA 20 71 0 AATAAAAATA 0.770196 -132 AATAATAAAGAATATGTTAAATTTTACCCT 21 8 0 AATATAAATT 0.886886 -213 ACATAAATAAAATAGCATGTATTTTTGGTGGTA 21 94 0 AATAAGTATT 0.192853 -127 TTTAAATTAAATTAAATTAAATTAAATGAGGAG 22 29 1 ATTATAAATT 0.257814 -224 ATTTGATATTAAAAGTTGAAATAATGTGTCAAA 22 178 1 AAAATAAATA 0.777871 -75 GATTTGTTGCAATAATTTAAATTAGAGATTTAA 23 23 1 AATATAAATT 0.895389 -66 ACCTTAATCAAATAAATAAAAATTAAAAAAGTC 23 66 0 AATATAAAAT 0.483373 -23 CCTAGACAAAAAAATATAAAATTAAGCAAAAAC 24 34 0 AAAATAAATT 0.798288 -145 TTTTTATCTTAATAATTAAAATTATAAAATAAG 24 67 1 AATATAAATT 0.895389 -112 AAAATTATAAAATAAGTTGTATAATGATGTTTG 24 84 1 AATATGTATA 0.329194 -95 TAAATTGTTTAAAAAAACAAATATAAAATTAAA 26 31 0 AAAAAAAATA 0.607672 -168 AAATAACCCGAAAAGGATAAATTGCTTTTGTTA 26 79 1 AAAAAAAATT 0.636524 -120 CAATCTCATTAAAACAAGAAATTTAAAATTAAA 29 102 0 AAAAAAAATT 0.636495 -83 **** * ***** Masking position 4 Map Score: 32.495 Number of sites scoring better than the average of aligned sites = 1253 Number in coding regions = 809 Number in noncoding regions = 444 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 12 ATTAACTCCTTATATATTTTCATT 6 57 0 ACTCCTTATA 0.834374 -14 ATAATCTCCTTATGGTAGTAACGC 7 38 0 TCTCCTTATG 0.831589 -14 AATTTACCCTTCTTATAATAAAA 8 7 0 CCTTCTTATA 0.812631 -17 GATGCCTCCTTATATATTCTATTA 13 227 0 CCTCCTTATA 0.974899 -14 TAACTTTTTACCTCCCTATGCTTTAATAAG 14 281 0 CCTCCCTATG 0.910001 -20 AAATCCTCCTAAAATTTAGGATAT 15 157 0 CCTCCTAAAA 0.812684 -14 CCTCCTTTAGAAAAATCAAA 19 12 0 CCTCCTTTAG 0.809617 -10 TCCTCCTTAAAACCAAATTAT 24 168 0 CCTCCTTAAA 0.960333 -11 ********** Masking position 3 Map Score: 1.90867 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 16 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ********** No masking Map Score: 7.77577e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 7.77577e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 7.77577e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0